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  • Turns out that plesiosaurs gave birth to live young. It’s about damned time.

    _Polycotylus latippinus_ mother giving birth to young in a very cetacean-like fashion. Illustration by: S. Abramowicz

    Just announced today in Science, researchers at the Marshall University and the Los Angeles County Museum described the presence of fossil young inside the body of the plesiosaur: Polycotylus latippinus. The results of their find seem to confirm what has been suspected for quite some time now, that plesiosaurs were viviparous animals.

    O’Keefe, F.R., Chiappe, L.M. 2011. Viviparity and K-Selected Life History in a Mesozoic Marine Plesiosaur (Reptilia, Sauropterygia). Science. Vol.333(6044):870-873

    The evidence had been mounting for some time now. While plesiosaurs came in numerous shapes and sizes, most of those sizes were in the large to giant range measuring in at multiple tonnes (e.g. Liopleurodon and Kronosaurus). That is a lot of weight to attempt to drag up on a beach for egg laying. Further, though the rib cage is well braced ventrally, the limb girdles are not braced against the vertebral column. This would make it very hard for a large landlubbing plesiosaur to make any kind of headway as the limbs would have no leverage against the body for dragging itself on land.

    Lastly, and perhaps most importantly, we have known of at least one plesiosaur fossil that had embryos in it. This has been known for at least five years now (I learned of it four years ago, and it has been hinted at before [Smith 2008]). Sadly this specimen still remains unpublished. This new paper by O’Keefe and Chiappe goes on to mention the relatively large size of the young, estimated at 1.5 meters when born. This was much larger than the young of other large extinct and extant marine reptiles. The authors (cautiously) suggest that this might hint at a different life history for plesiosaurs vs. other marine reptiles. They posit that plesiosaurs might have nurtured a small amount of relatively large young, which in turn might have meant that they were more social than previously thought.

    Naturally this has resulted in the inevitable comparison to whales. While a “pod of plesiosaurs” does sound interesting, we have far too little evidence to say if such a thing ever happened (and the authors state this too). What we do know is that young plesiosaurs have been found in shallow marine settings. These have been posited to have been “nurseries” where young could stay out of sight from predators while reaching adult size (Martin et al. 2007). Whether, or not adults stayed around, or if they joined a “pod” later (if at all) is all unknown. Still, it is nice to see some validation to what seemed almost necessary for so long.

    Admittedly not everyone is convinced (a good thing to see in science). Dr. Ken Carpenter of the Utah State Museum offered Science magazine a dissenting view, suggesting that the position of the young could still indicate that these were juveniles that had been eaten. The O’Keefe and Chiappe considered this in the paper and pointed out that the skeletons lacked any signs of acid etching, as well as showed numerous skeletal bones that did not appear fully ossified. Further analysis could shed more light on this. Publishing on that other plesiosaur could really help things out too.

    Viviparity - could these guys be next? Image from the Nature Museum in Stuttgart.

    Assuming that we are looking at viviparous plesiosaurs, that just leaves two other large marine reptile groups of the Mesozoic. Turtles and Crocodylomorphs. In both cases we have extant animals that are obligate oviparous animals, but there might still be reason to think that live birth might have evolved in these groups too.  Again, much like with the plesiosaurs, the groups in question (protostegid sea turtles and the podocnemid Stupdendemys, as well as metriorhynchid crocodylomorphs) have members that grew extremely large. While Protostega gigas may have been able to haul itself out on land as extant leatherbacks (Dermochelys coriacea) do, it seems harder to justify that in the much larger Archelon ischyros; an animal that has been estimated to tip the scales at 2 tonnes. Given the amount of effort it takes a large female leatherback  (~1 tonne) to haul herself up and down a beach (not to mention the damage it causes to the animals in the short term), it would be all the more amazing if A.ischyros was able to pull off such a feat. The same would go for the metriorhynchids, who had adapted completely to a marine lifestyle (i.e. they had flippers and a tailfin). If a 5 meter Gavialis gangeticus can barely move around on land, I’d hate to see what a 5 meter Dakosaurus would look like. To date we have no evidence one way, or the other for these last two groups. There is a bit more resistance to the idea of viviparity in these groups as no extant members exhibit viviparity. This has lead some to wonder if the calcified eggs of archosaurs (and many chelonians) might prove a phylogenetic constraint on live bearing (the young absorb calcium from the shell, which could mess up calcium absorption in a taxon evolving along the lines of viviparity). The chelonian shell — in turn — may also have been constraining on the size of young that can be held in the body cavity. Still, to date, there are no nests, eggs, or embryos for any of these taxa, thus leaving the matter open for debate. It is interesting that neither protostegids, nor metriorhynchids got to the huge sizes of mosasaurs, ichthyosaurs and plesiosaurs, but that could have been for any number of reasons including the simple lack of finding the larger taxa yet.  Until then the physics vs. phylogeny argument remains unresolved.

    Anyway, compelling evidence for live bearing in at least some plesiosaurs. Woohoo!

    ~Jura

    References

    Martin, J., Sawyer, F., Reguero, M. Case, J.A. 2007. Occurrence of a Young Elasmosaurid Plesiosaur Skeleton from the Late Cretaceous (Maastrichtian) of Antarctica. 10th Int.Symp.Antarctic Earth Sciences.
    O’Keefe, F.R., Chiappe, L.M. 2011. Viviparity and K-Selected Life History in a Mesozoic Marine Plesiosaur (Reptilia, Sauropterygia). Science. Vol.333(6044):870-873
    Smith, A.S. 2008. Fossils Explained 54: Plesiosaurs. Geol.Today. Vol.24(2):71-75

     


  • The 3D alligator

    Model organisms are a staple of biology. They are taxa that are used to answer larger questions about that group as a whole, or some general biological problem. Model organisms are chosen for their ease of handling, cheap acquisition, generally “generic” structures, or all of the above. Every major class has a model organism to represent it. Just among vertebrates we have:

     

    A stillborn hatchling rests inside the left nostril of a large 3.7m (12ft) adult which is some 5000 times larger!
    A stillborn hatchling rests inside the left nostril of a large 3.7m (12ft) adult which is some 5000 times larger!

    Mammals with mice (Mus musculus), dogs (Canis familiaris [or Canis lupus familiaris if you lean that way]), cats (Felis catus [or Felis sylvestris catus for the same reason as dogs]), guinea pigs (Cavia porcellus) and rhesus monkeys (Macaca mulatta).

    Birds with chickens (Gallus gallus), pigeons (Columba livia), and zebrafinch (Taeniopygia guttata).

    Ray finned fish with zebrafish (Danio rerio), swordtails (Xiphophorous) and cichlids (Cichlidae).

    Amphibians with the African clawed frog (Xenopus laevis), and axolotol (Ambystoma mexicanum).

    Reptiles with anoles (Anolis), fence lizards (Sceloporous), painted turtles (Chrysemys picta) and finally, the American Alligator (Alligator mississippiensis).

    Alligators are relatively new to the model organism realm, but they have proven to be extremely informative. They seem to the be most even tempered of extant crocodylians, making them “more safe” for researchers to work with. Hatchlings start off as miniscule 68 gram (0.15 lbs) animals that later can grow to 363 kg (800 lbs) adults, passing through an enormous size range throughout ontogeny. This growth rate is very food dependent, making it possible to raise alligators almost as bonsai trees. Also, with their unique position on the organismal family tree, alligators are one of the closest living relatives to dinosaurs. Along with birds, they have the potential to help constrain our assumptions about dinosaurs; thus making them very popular subjects for paleontological research as well.

    Today, alligators get to make one more stamp on human knowledge with the release of the 3D alligator project from the Holliday and Witmer labs.

    Researchers from both labs went through the painstaking process of digitizing the skulls of an adult and a hatchling American alligator, and then digitally separated each bone. The result is a 3D model that can have each bone turned on and off at will. The neat thing is that both labs have made these data freely available for anyone to look at, and download as 3D pdfs, wirefusion models, and multiple movies.

    So if one every wanted to know just how many bones make up a crocodylian skull, or how each bone aligns to each other, I highly recommend downloading the 3D pdfs of the adult and hatchling. Not only will one learn all the different bones that compose the skull, but by comparing hatchling to adult, one can see just how radically these bones change throughout ontogeny.

    It’s neat, free, informative and reptilian. What more can one ask for. 🙂

    ~Jura


  • Metabolism part I: The importance of being specific

    From archaea to blue whales. Metabolism is a hallmark of all living things

    Metabolism, and metabolic rate tend to feature pretty highly in literature related to dinosaurs and other reptiles. For instance it is often stated that reptiles have metabolic rates around 1/10th those of similar sized mammals and birds, but what exactly does that mean? Talks of thermoregulation focus heavily on the role of metabolism, while allometric studies focus on how metabolism is affected by size. Given the prevalence of metabolic terminology in dinosaur and reptile papers/books, I thought it might be best to quickly give a review of metabolism, metabolic studies, and what all of that means for real animals.

    Metabolism is everything


    Metabolism is defined as the sum total energy expenditure of an organism. That is to say metabolism is the total energy an organism uses during its life. It is often broken up into the chemical reactions that build up resources (anabolism) and the reactions that break those resources down (catabolism).  The amount of metabolism, or energy expenditure during a specific interval of time (seconds to days) is referred to as metabolic rate. From bacteria to blue whales, metabolism is the measure of all the energy that lets these critters go, and metabolic rates determine how much energy that is going to take. It can be measured in a variety of ways from respirometry to doubly labeled water and heart rate telemetry. The diversity of metabolic rate measurements is reflected in the units used to measure metabolism; which can range from watts/hour to milliliters of oxygen per minute, and even to joules per second.

    Specificity is important


    A key thing about metabolic rates is that they are plastic. They change depending on the situation presented. For instance one could measure the metabolic rate of a sleeping cat, and then compare it to measurements from that same cat while playing, or after eating a big meal. Metabolic rates ramp up when energy demand increases, and then ramp down when that energy demand decreases, or when the environment demands drastic energy cuts (e.g. starvation). Thus when measuring the metabolic rate of an animal it is important to decide exactly what kind of metabolic rate you are trying to measure.

    And boy, oh boy are there a lot of different flavours to choose from.

    One can measure: BMR, SMR, RMR, MMR, AMR, and FMR just for starters.

    Those are a lot of initialisms, and they are just the most common ones. The choice of metabolic rate that one decides to measure is also going to dictate the technique that will be employed. So what do all these things stand for, and what technique is best for what? Let’s find out.
    Continue reading  Post ID 870


  • Nile crocodile takes on elephant

    The site has been pretty slow for the past couple of months as academic life has eaten up a lot of my free time. That should change in a few weeks (and I do have a doozy of a post I have been working on).

    For now though I leave folks with this amazing photographic account of a Nile crocodile (Crocodylus niloticus) attacking an adult mother elephant (Loxodonta africana).

    Photos by Martin Nyfeler. Be sure to click on the image for the full account of what took place (complete with more photos)

    Whether, or not the crocodile meant to try this, or if this was an accidental predation attempt remains unknown. While this might be the first time this was caught on film, it is not the only account of this. Nile crocs have been known to attempt to take down large elephants by grabbing onto their trunks. The initial attack is almost always unsuccessful, but if the croc winds up doing enough damage it can result in the elephant dying days later (as a broken trunk pretty much limits all access to food). Not sure if the crocs ever benefit from this, but the fact that they can kill large adults is enough to make them a formidable threat to any thirsty elephant.


  • T-U-R-T-L-E Power Part 3: Leatherbacks Break All the Rules.

    Leatherbacks are already viewed as unique, but you might be surprised at just how strange this species really is. Picture from: amigosdomarnaescola.com

    Continuing the series, let us now take a look at one weird turtle species in particular: Dermochelys coriacea, the leatherback sea turtle.

    While the utter weirdness of D.coriacea is ultimately the main reason for why it wound up in this series, there is an ulterior motive. Having searched the internet for general information on the species I found myself rather disappointed with the amount of utterly generic / wrong info regarding leatherbacks. Its Wikipedia entry is particularly disappointing. So here’s hoping this influx of information can help alleviate that.

    A turtle without a shell?

    Yes, it’s true, leatherback turtles have lost their shells. Shell reduction is relatively common in turtles. It seems a little funny. After going through all the trouble of evolving impregnable armour, many taxa then went out and removed large chunks of it. We see shell reduction in snapping turtles (Chelydra and Macrochelys), soft-shelled turtles, and even other sea turtles. None of them, however, reduced their shells to the point of actually removing them.

    In leatherbacks the “shell” is nothing more than a loose collection of osteoderms spread over the back and belly. There is no longer a definitive carapace, or plastron. In fact leatherbacks don’t even produce Beta-keratin (the hard component of reptile scales). Instead this has all been replaced by thick, leathery skin.

    Continue reading  Post ID 870


  • T-U-R-T-L-E Power! Part 2: The weird and wacky origin of turtles.

    A Galapagos tortoise struts about, secure in the knowledge that no one will ever know where the hell it came from. Photo from petcaregt.com

    This is a long overdue follow up to my original Turtle Power article back in…yeah never mind the date.

    As established previously, turtles are a strange, and highly diverse group of animals, but how did they come to be this way?

    The turtle bauplan has been a phylogenetic double edged sword. On the one hand, the unique shell design, and the necessary body contortions associated with it, make chelonians a very easy group to classify. However, it is these same peculiarities that keep us from finding the ancestor to turtles. To date, there are no “half-turtles.” No good transitionals between one reptile group to that  of turtles. As such, the list of turtle ancestors runs all over Reptilia. Some paleontologists believe the origin lies at the base with reptiles like procolophonoids, and pareiasaurs. Others believe turtles are a bit more closely related to extant reptiles, and belong in, or alongside the sauropterygians (plesiosaurs, nothosaurs, and placodonts). There is even some evidence to suggest turtles are actually in the same reptile group as dinosaurs and crocodylians (Archosauria).

    Curse that shell! - Photo by tompain

    How can the list be this extensive? Read on to find out.

    Continue reading  Post ID 870


  • Get in on the deal: Indiana University Press one day sale.

    I apologize ahead of time for what will likely sound like spam, but:

    Just a quick post to remind folks that today, and only today, Indiana University Press is offering a 60% off sale on all their books. That includes their famed Life of the Past series.

    So if you have yet to get your copy of The Complete Dinosaur, or have been itching to snag the most comprehensive book ever written on Deinosuchus, ankylosaurs, or mosasaurs, but didn’t have the necessary funds; now is your chance to get them for cheap.

    Just remember, the sale ends today.

    ~Jura


  • New study shows that gators are one-way breathers too.

    I would be remiss not to talk about this amazing discovery published last week in Science.

    Farmer,C.G. & Sanders,K. 2010. Unidirectional Airflow in the Lungs of Alligators. Science. vol.327:338-340

    The anatomical similarities of alligators and birds has been known for quite some time (at least 100 years), and this anatomical similarity extends down into the lungs. Though alligators lack the pneumatic carvings of the post-cranial skeleton (air sacs) that are seen in birds, saurischian dinosaurs and pterosaurs; their lungs and bronchi do share the same structural features.

    Birds have a unique lung design that allows air to pass through it in a single direction. Unlike mammals, there is no “dead end” to the avian lung. This provides the benefit of a constant supply of highly oxygenated air to the lung tissue; which allows for more efficient gas exchange. Up until last week, this lung design was thought to be a hallmark of birds, and possibly saurischian dinosaurs, and pterosaurs.

    Well it turns out that this unique avian synapomorphy is a heck of a lot older than we thought.

    Dr. Colleen Farmer, and Kent Sanders M.D. of the University of Utah, considered the uncanny anatomical similarities of the avian and crocodylian lung, and wondered if these similarities extended to the physiology too. In other words: If it looks like a unidirectional lung, does it also function like one?

    Farmer & Sanders set to work by removing the lungs of four dead alligators donated to her lab. They pumped air through them, and monitoring the direction in which it traveled (using flowmeters). They then surgically inserted flowmeters into anesthetized alligators, and measured the airflow direction in living animals. Lastly, to drive the point across completely, they filled up an excised lung with fluid that contained fluorescent beads, and proceeded to pump the water in and out. This last test was recorded, and three movies of it, were made available to the public. They can be viewed here. Three was probably overkill though, as once you’ve seen fluorescent beads move one way in a gator lung, you’ve seen them all. : )

    The results showed conclusively that alligator lungs pump air through them in one direction only. The repercussions of this find are actually pretty enormous. For starters, the similarity in anatomy and physiology of avian and crocodylian lungs, suggests that they are homologous. This would mean that both groups inherited these lungs from a common ancestor. This means that it was highly likely that all dinosaurs, pterosaurs, rauisuchians, aetosaurs, phytosaurs and the myriad of other archosaurs that graced this planet some 200 million years ago, housed this particular flow-through style lung.

    It also helps put to rest arguments about air sac functions. It has long been argued that the presence of a unidirectional lung, necessitates the presence of air sacs to “pump the air in.” (air sacs offer zero, or next to zero gas exchange potential, so there is no actual breathing going on in them). A lack of air sacs in ornithischian dinosaurs, has been used to suggest that their pulmonary physiology was more like mammals and lizards, than it was like birds (Ruben et al 1999). Data from previous research (O’Connor & Claessens 2005) has cautioned that the presence of air sacs does not guarantee the existence of a flow through system. These latest data now show us that a flow-through system can, and likely did, evolve without the “need” for an air sac pump.

    CT scan of alligator, with 3D reconstruction of lungs. For more details on what the colours mean, click the picture.

    Exactly how all of this works, is still not understood. The “hepatic piston” diaphragmatic pump of crocodylians is well known, and is likely the ultimate driver of respiration in these animals, but the nuts & bolts of how all this unidirectional flow takes place (the fluid dynamics of the lung) remains a mystery. One question that would be worthy of a follow up study (which the author’s have hinted at doing) is whether, or not a cross-current, or counter-current system (where deoxygenated blood flows perpendicular, or opposite the direction of highly oxygenated air) is present in crocodylians too.  A cross-current system is found in birds. Is that unique to them, or was this also a phylogenetic “hand-me-down?” Hopefully now, with this new discovery, future research will be done on the crocodylian lung, to further understand how it actually works.

    Ultimately that is the biggest piece of news to come out of this paper. For well over 100 years, the crocodylian lung was just assumed to be a “dead-end” space that worked in a manner similar to that of mammals. It wasn’t until someone actually thought “what do we really know about this structure” did we find something quite the opposite taking place. This is hardly the first time that this has happened either (for instance). As I have mentioned (ranted/harped on) before, reptiles tend to get the short end of the stick when it comes to a lot of biological and paleontological studies (especially if they involve comparison between broad animal groups [classes]). I’m always amazed (though rarely surprised) when a study that actually looks into commonly held assumptions about these critters, finds said assumptions to be quite off the mark. Here’s hoping that we continue to see future studies like this, go on.

    In the end, all of this brings us closer to the truth about how life really works; which is why we do all of this stuff in the first place.

    ~Jura

    References


    Farmer,C.G. & Sanders,K. 2010. Unidirectional Airflow in the Lungs of Alligators. Science. vol.327:338-340

    O’Connor, P.M.& Claessens, A.M. 2005. Basic Avian Pulmonary Design and flow-Through Ventilation in Non-Avian Theropod Dinosaurs. Nature. Vol. 436:253-256.

    Ruben, J.A., Dal Sasso, C., Geist, N.R., Hillenius, W.J., Jones, T.D. 1999. Pulmonary Function and Metabolic Physiology of Theropod Dinosaurs. Science. Vol.283(5401):514-516.


  • Mechanics of bipedalism suggest dinosaurs had to be warm-blooded. Or: Why the aerobic capacity model needs to be retired.

    The old "cold blooded or warm blooded" argument once again rears its ugly head.

    [Editor’s note: A response from the authors can be found here. It answers many of the questions I had about the paper, though I feel the biggest question remains open for debate. I appreciate the authors taking their time to answer my questions, and PLoS ONE for allowing this type of open communication.]

    This post has taken an inordinate amount of time to write up. Mostly because it required finding enough free time to sit down and just type it out.  So I apologize ahead of time for bringing up what is obviously old news, but I felt this paper was an important one to talk about, as it relied on a old, erroneous, but very pervasive, popular and rarely questioned hypothesis for how automatic endothermy (mammal and bird-style “warm-bloodedness”) evolved.

    Back in November, a paper was published in the online journal: PLoS ONE. That paper was:

    Pontzer, H., Allen, V. & Hutchinson, J.R. 2009. Biomechanics of Running Indicates Endothermy in Bipedal Dinosaurs. PLoS ONE.Vol 4(11): e7783.

    Using muscle force data for the hindlimbs of theropods, and applying it to a model based on Pontzer (2005, 2007), the authors were able to ascertain the approximate aerobic requirements needed for large bipedal theropods to move around. Their conclusion was that all but the smallest taxa had to have been automatic endotherms (i.e. warm-blooded).

    Time to stop the ride and take a closer look at what is going on here.

    In 2004, John Hutchinson – of the Royal Veterinary College, London UK – performed a mathematical study of bipedal running in extant taxa. He used inverse dynamics methods to estimate the amount of muscle that would be required for an animal to run bipedally. He then tested his models on extant animals (Basiliscus, Iguana, Alligator, Homo, Macropus, Eudromia, Gallus, Dromaius, Meleagris, and Struthio). The predictive capacity of his model proved to be remarkably substantial and stable (Hutchinson 2004a).  A follow up paper in the same issue (Hutchinson 2004b) used this model to predict bipedal running ability in extinct taxa (Compsognathus, Coelophysis, Velociraptor, Dilophosaurus, Allosaurus, Tyrannosaurus and Dinornis).  Results from this study echoed previous studies on the running ability of Tyrannosaurus rex (Hutchinson & Garcia 2002), as well as provided data on the speed and agility of other theropod taxa.

    The difference between effective limb length and total limb length in the leg of Tyrannosaurus rex

    Meanwhile in 2005, Herman Pontzer – of Washington University in St. Louis, Missouri – did a series of experiments to determine what was ultimately responsible for the cost of transport in animals. To put it another way: Pontzer was searching for the most expensive thing animals have to pay for in order to move around. One might intuitively assume that mass is the ultimate cost of transport. The bigger one gets, the more energy it requires to move a given unit of mass, a certain distance. However experiments on animals found the opposite to be the case. It actually turns out that being bigger makes one “cheaper” to move.  So then what is going on here?

    Pontzer tested a variety of options for what could be happening; from extra mass, to longer strides. In the end Pontzer found that the effective limb length of animals, was ultimately the limiting factor in their locomotion. Effective limb length differs from the entirety of the limb. Humans are unique in that our graviportal stance has us using almost our entire hindlimbs. Most animals, however, use a more crouched posture that shrinks the overall excursion distance of the hindlimb (or the forelimb). By taking this into account Pontzer was able to find the one trait that seemed to track the best with cost of transport in animals over a wide taxonomic range (essentially: arthropods – birds).

    This latest study combines these two technique in order to ascertain the minimum (or approx minimum) oxygen requirements bipedal dinosaurs would need in order to walk, or run.

    As with the previous papers, the biomechanical modeling and mathematics are elegant and robust. However, this paper is not without its flaws. For instance in the paper the authors mention:

    We focused on bipedal species, because issues of weight distribution between fore and hindlimbs make biomechanical analysis of extinct quadrupeds more difficult and speculative.

    Yet this did not stop the authors from applying their work on bipeds, to predicting the maximum oxygen consumption of quadrupedal iguanas and alligators. No justification is ever really given for why the authors chose to do this. Making things even more confusing, just a few sentences later, it is mentioned (ref #s removed to avoid confusion):

    Additionally, predicting total muscle volumes solely from hindlimb data for the extant quadrupeds simply assumes that the fore and hindlimbs are acting with similar mechanical advantage, activating similar volumes of muscle to produce one Newton of GRF. This assumption is supported by force-plate studies in other quadrupeds (dogs and quadrupedal chimpanzees)

    The force plate work cited is for quadrupedal mammals. However, mammals are not reptiles. As Nicholas Hotton III once mentioned (1994), what works for mammals, does not necessarily work for reptiles. This is especially so for locomotion.

    In many reptiles (including the taxa used in this study) the fore and hindlimbs are subequal in length; with the hindlimbs being noticeably longer and larger. Most of the propulsive power in these reptiles comes from the hindlimbs (which have the advantage of having a large tail with which to lay their powerful leg retractor on). The result is that – unlike mammals – many reptiles are “rear wheel drive.”

    The last problem is by far the largest, and ultimately proves fatal to the overall conclusions of the paper. The authors operated under the assumptions of the aerobic capacity model for the evolution of automatic endothermy.

    It is here that we come to the crux of the problem, and the main subject of this post.

    Continue reading  Post ID 870


  • 2.9 upgrade

    Recently went through the hoopla involved with getting WordPress upgraded (needed to upgrade the MySQL database). Everything appears in working order, barring some strange “?” symbols. I’ll have to figure that out later.